Chinese Bulletin of Botany ›› 2020, Vol. 55 ›› Issue (6): 715-732.DOI: 10.11983/CBB20091
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Yuhui Zhao1, Xiuxiu Li1,2, Zhuo Chen1,2, Hongwei Lu1,2, Yucheng Liu1,2, Zhifang Zhang1,2, Chengzhi Liang1,2,*()
Received:
2020-05-20
Accepted:
2020-08-26
Online:
2020-11-01
Published:
2020-11-11
Contact:
Chengzhi Liang
Yuhui Zhao, Xiuxiu Li, Zhuo Chen, Hongwei Lu, Yucheng Liu, Zhifang Zhang, Chengzhi Liang. An Overview of Genome-wide Association Studies in Plants[J]. Chinese Bulletin of Botany, 2020, 55(6): 715-732.
Method | Population structure | Kinship | Precision | Characteristic | Computational speed | Statistical power | Application |
---|---|---|---|---|---|---|---|
Standard MLM | P | All markers | Low | High | >100 papers | ||
GRAMMAR | P | Approximate method | Very fast | Intermediate | Barley (200) | ||
EMMA | P | Exact method | Intermediate | Similar to Standard MLM | >100 papers | ||
EMMAX | P | All markers | Approximate method | High marker densities | Fast | Similar to Standard MLM | >100 papers |
CMLM | P | Large sample sizes | Better than Standard MLM | >100 papers | |||
FaST-LMM | P | A subset of genetic markers | Exact method | Large sample sizes | Fast | Similar to Standard MLM | Rice (200?1500) |
GEMMA | P | Exact method | Fast | Similar to Standard MLM | Arabidopsis thaliana (190-500) | ||
ECMLM | P | Intermediate | Better than Standard MLM | Sorghum (250-350), soybean (200-400), wheat (250-300) | |||
GRAMMAR- Gamma | P | Approximate method | High marker densities | Fast | Similar to Standard MLM | Oilseed rape (200) | |
SUPER | P | Trait-associated markers | Large sample size & high marker density | Fast | Better than Standard MLM | Wheat (300-400) | |
Farm-CPU | P | A subset of genetic markers | Approximate method | Large sample size & high marker density | Fast | Better than Standard MLM | Wheat (100-1200), maize (100-5000) |
BLINK | P | A subset of genetic markers | Approximate method | Large sample size & high marker density | Faster than FarmCPU | Better than FarmCPU |
Table 1 Performance comparison of different methods in mixed linear model (MLM)
Method | Population structure | Kinship | Precision | Characteristic | Computational speed | Statistical power | Application |
---|---|---|---|---|---|---|---|
Standard MLM | P | All markers | Low | High | >100 papers | ||
GRAMMAR | P | Approximate method | Very fast | Intermediate | Barley (200) | ||
EMMA | P | Exact method | Intermediate | Similar to Standard MLM | >100 papers | ||
EMMAX | P | All markers | Approximate method | High marker densities | Fast | Similar to Standard MLM | >100 papers |
CMLM | P | Large sample sizes | Better than Standard MLM | >100 papers | |||
FaST-LMM | P | A subset of genetic markers | Exact method | Large sample sizes | Fast | Similar to Standard MLM | Rice (200?1500) |
GEMMA | P | Exact method | Fast | Similar to Standard MLM | Arabidopsis thaliana (190-500) | ||
ECMLM | P | Intermediate | Better than Standard MLM | Sorghum (250-350), soybean (200-400), wheat (250-300) | |||
GRAMMAR- Gamma | P | Approximate method | High marker densities | Fast | Similar to Standard MLM | Oilseed rape (200) | |
SUPER | P | Trait-associated markers | Large sample size & high marker density | Fast | Better than Standard MLM | Wheat (300-400) | |
Farm-CPU | P | A subset of genetic markers | Approximate method | Large sample size & high marker density | Fast | Better than Standard MLM | Wheat (100-1200), maize (100-5000) |
BLINK | P | A subset of genetic markers | Approximate method | Large sample size & high marker density | Faster than FarmCPU | Better than FarmCPU |
Figure 4 Genome-wide association study (GWAS) results of 721 rice accessions for heading date (A) Manhattan plots of GWAS results for heading date; (B) QQ plot; (C) Local manhattan plots and LD heatmap around the peak on chromosome 6. Candidate region was labelled by red dotted line while the black dotted line indicated threshold -log10 (P)=7.80.
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